General information for g5489.t39
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5489 is located on chr_2: 9846707..9847795 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_2 | g5489 | g5489.t39 | isoform | g5489.t39 | 9846707 | 9847795 |
| chr_2 | g5489 | g5489.t39 | exon | g5489.t39.exon1 | 9846707 | 9846882 |
| chr_2 | g5489 | g5489.t39 | exon | g5489.t39.exon2 | 9846932 | 9847795 |
| chr_2 | g5489 | g5489.t39 | cds | g5489.t39.CDS1 | 9847439 | 9847795 |
| chr_2 | g5489 | g5489.t39 | TSS | g5489.t39 | NA | NA |
| chr_2 | g5489 | g5489.t39 | TTS | g5489.t39 | NA | NA |
Sequences
>g5489.t39 Gene=g5489 Length=1040
ATGGGTAATAATAAAAAGAGACGTCCTCATCATAAGAAAAAAGGTAACTCTCAGAGTGCT
CAAACTGACACAAATAAGCATACAGCTGCAGGACTTGCCGAAAATAATGAGCAAGCTCAA
GAGAAGGAGGACAAGATTGAAGAAGTTTCAAAAGCATTGAAAAGTGAAAATGTATTATTA
GAATCGGAAAAAGTAGCCAAAGTTGAAAAAGAGGCTGAAGAAGGAAATAAAAATGAGAAA
GAAAATAATATTGAAATAGAAAAGAATGAGATCAAGTCTGAAAAGCAGCAAACTAAGAAG
GATGAAAATCCTACAGTCAAGAAAGATGACAAAGCGCCACTTGAGGTAAATCATTAACTG
AAAATTTTCATTTTAACATGATTAACTTTTTTTTCACTTGACATAAAACTTGAGTCAAGT
AGAAAAGTGAATTGTTGTTGTGTTGTGTAGCAGTGCAGTCAAGTCGTCAAACGAGCTTAA
TCGAAATGAGCAGTGAAATTTCGGAAAAATTAGAAAATTTGGATATAGAATCGAATCAGG
CATGAGATAATAGTTAATTTTAATAATGTTATTCTCAACATTTCAAAAAATAATTAATTT
AAATAAGTTTATTGTGGTAAATCAACTGAAAAGTGGAAATTGGAATCGGCAATGTTTTGC
AACTTTGGTTCGTGATGATCGCTTTAAAAACTATAATTTGATAGATTTAGTGATACATTA
ATACACTTTGAGTTATGCTTATAACATACAATGTTATTAATCTTTGTTTTATTTTATTTG
ACCTAATTTTCATTTTTCCACGTTGATTTCATTCCATAAATTTTTCTCATTCCTTAAACA
AAACAAATATTACGTCAGACATTTTCATCATAATTTTAGGCCGCAAAACAAAAGGCTGCG
AAAAAGAAGAAACAGGAAGAAATGGGTGTTGAAACAGGTTAGATATTTTTTGCAAAAGCT
CTTTCTTTTATTACGTGCGTAAATCTGCAGACAGCCAACTCATCATATATGATTTATATC
ATCTTTTTAGGAATTAAAGA
>g5489.t39 Gene=g5489 Length=118
MGNNKKRRPHHKKKGNSQSAQTDTNKHTAAGLAENNEQAQEKEDKIEEVSKALKSENVLL
ESEKVAKVEKEAEEGNKNEKENNIEIEKNEIKSEKQQTKKDENPTVKKDDKAPLEVNH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5489.t39 | Coils | Coil | Coil | 29 | 59 | - |
| 5 | g5489.t39 | Coils | Coil | Coil | 69 | 101 | - |
| 1 | g5489.t39 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 118 | - |
| 2 | g5489.t39 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 15 | - |
| 4 | g5489.t39 | MobiDBLite | mobidb-lite | consensus disorder prediction | 18 | 35 | - |
| 3 | g5489.t39 | MobiDBLite | mobidb-lite | consensus disorder prediction | 37 | 118 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5489/g5489.t39; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5489.t39.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
